Fabio Franchino
Protein-ligand binding and investigation of flexibility shifts with computational tools.
Rel. Cecilia Surace, Domenico Scaramozzino. Politecnico di Torino, Corso di laurea magistrale in Ingegneria Biomedica, 2026
Abstract
Proteins are intrinsically dynamic entities whose biological function depends on their ability to undergo conformational transitions and on their internal dynamics, which can be modulated by ligand binding. This work aims to study how the protein--ligand binding effect influences flexibility through a computational approach based on Elastic Network Models (ENM) and Normal Mode Analysis (NMA). The analysis employs the RESPEC model, which represents the protein--ligand complex with a hybrid resolution: the protein is described using a coarse-grained approach at the $C_\alpha$ level, whereas the ligand is modeled at atomic resolution. The implementation of the model used in this work was validated by comparing the obtained results with those reported in the literature, thereby identifying a robust set of parameters for the subsequent analyses ($\delta_U = 22\,\si{\angstrom}$, $\delta_{PL} = 12\,\si{\angstrom}$, $p=1$).
A key point of the work concerns the impact of the choice of the global parameter $\gamma_0$: either set to unity or calculated through fitting to experimental B-factors
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